Variant report

Variant	rs7986369
Chromosome Location	chr13:48463123-48463124
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12869557	0.95[ASN][1000 genomes]
rs12873785	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555722	0.97[ASN][1000 genomes]
rs17425881	0.89[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs1974039	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2104373	0.97[ASN][1000 genomes]
rs2104374	0.96[ASN][1000 genomes]
rs2296573	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs4553498	0.96[ASN][1000 genomes]
rs4942710	0.97[ASN][1000 genomes]
rs6561411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7317860	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7323277	0.97[ASN][1000 genomes]
rs7334095	0.95[ASN][1000 genomes]
rs7334463	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7336952	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7337766	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7981260	0.95[ASN][1000 genomes]
rs7993360	0.94[ASN][1000 genomes]
rs7993810	1.00[ASN][1000 genomes]
rs7994427	0.97[ASN][1000 genomes]
rs7998886	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316346	0.84[JPT][hapmap]
rs9562779	0.97[ASN][1000 genomes]
rs9567940	0.96[ASN][1000 genomes]
rs9567943	0.99[ASN][1000 genomes]
rs9567948	0.91[ASN][1000 genomes]
rs9595813	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7986369	MED4	cis	multi-tissue	Pritchard
rs7986369	MED4	cis	cerebellum	SCAN
rs7986369	SERP2	cis	cerebellum	SCAN
rs7986369	SPERT	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48449000-48464200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:48453800-48471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:48454800-48464400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:48457200-48478000	Weak transcription	Adipose Nuclei	Adipose
6	chr13:48460800-48464600	Weak transcription	HSMMtube	muscle
7	chr13:48461000-48464200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:48461000-48464200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:48461000-48472200	Weak transcription	Spleen	Spleen
10	chr13:48461000-48472400	Weak transcription	Lung	lung
11	chr13:48461000-48478200	Weak transcription	Left Ventricle	heart
12	chr13:48461600-48464200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:48461800-48463800	Weak transcription	Dnd41	blood

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